when i run:
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux.qza
–p-trunc-len-f 0
–p-trunc-len-r 280
–p-trim-left-f 5
–p-trim-left-r 5
–o-representative-sequences rep-seqs.qza
–o-table table.qza
half an hour later:
Plugin error from quality-filter:
Argument to parameter ‘demux’ is not a subtype of SampleData[SequencesWithQuality].
Debug info has been saved to /tmp/qiime2-q2cli-err-gngaj7ze.log
log file:
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: run_dada_paired.R /tmp/tmpcmlklyrt/forward /tmp/tmpcmlklyrt/reverse /tmp/tmpcmlklyrt/output.tsv.biom /tmp/tmpcmlklyrt/filt_f /tmp/tmpcmlklyrt/filt_r 0 280 5 5 2.0 2 consensus 1.0 1 1000000
R version 3.3.2 (2016-10-31)
Loading required package: Rcpp
There were 50 or more warnings (use warnings() to see the first 50)
DADA2 R package version: 1.4.0
- Filtering …
- Learning Error Rates
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 179, in denoise_paired
run_commands([cmd])
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 35, in run_commands
subprocess.run(cmd, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpcmlklyrt/forward’, ‘/tmp/tmpcmlklyrt/reverse’, ‘/tmp/tmpcmlklyrt/output.tsv.biom’, ‘/tmp/tmpcmlklyrt/filt_f’, ‘/tmp/tmpcmlklyrt/filt_r’, ‘0’, ‘280’, ‘5’, ‘5’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status -9
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/commands.py”, line 218, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 220, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 355, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2017.10/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 194, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
I have try uninstall R of my windows env, and update R in VBox, it also didn’t work, can somebody help me? thank you in advance